Computational Methods in Systems Biology

Table of Contents
Modal Logics for Brane Calculus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
M. Miculan, G. Bacci
Deciding Behavioural Properties in Brane Calculi . . . . . . . . . . . . . . . . . . . . . 17
N. Busi
Probabilistic Model Checking of Complex Biological Pathways . . . . . . . . . . 32
J. Heath, M. Kwiatkowska, G. Norman, D. Parker,
O. Tymchyshyn
Type Inference in Systems Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
F. Fages, S. Soliman
Stronger Computational Modelling of Signalling Pathways Using Both
Continuous and Discrete-State Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
M. Calder, A. Duguid, S. Gilmore, J. Hillston
A Formal Approach to Molecular Docking . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
D. Prandi
Feedbacks and Oscillations in the Virtual Cell VICE . . . . . . . . . . . . . . . . . . 93
D. Chiarugi, M. Chinellato, P. Degano, G. Lo Brutto,
R. Marangoni
Modelling Cellular Processes Using Membrane Systems with Peripheral
and Integral Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
M. Cavaliere, S. Sedwards
Modelling and Analysing Genetic Networks: From Boolean Networks
to Petri Nets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
L.J. Steggles, R. Banks, A. Wipat
Regulatory Network Reconstruction Using Stochastic Logical
Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
B. Wilczy ́ski, J. Tiuryn
n
Identifying Submodules of Cellular Regulatory Networks . . . . . . . . . . . . . . . 155
G. Sanguinetti, M. Rattray, N.D. Lawrence
Incorporating Time Delays into the Logical Analysis of Gene Regulatory
Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
H. Siebert, A. Bockmayr
A Computational Model for Eukaryotic Directional Sensing . . . . . . . . . . . . 184
A. Gamba, A. de Candia, F. Cavalli, S. Di Talia, A. Coniglio,
F. Bussolino, G. Serini
Modeling Evolutionary Dynamics of HIV Infection . . . . . . . . . . . . . . . . . . . . 196
L. Sguanci, P. Li`, F. Bagnoli
o
Compositional Reachability Analysis of Genetic Networks . . . . . . . . . . . . . . 212
G. G ̈ssler
o
Randomization and Feedback Properties of Directed Graphs Inspired
by Gene Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
M. Cosentino Lagomarsino, P. Jona, B. Bassetti
Computational Model of a Central Pattern Generator . . . . . . . . . . . . . . . . . 242
E. Cataldo, J.H. Byrne, D.A. Baxter
Rewriting Game Theory as a Foundation for State-Based Models of
Gene Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
C. Chettaoui, F. Delaplace, P. Lescanne, M. Vestergaard,
R. Vestergaard
Condition Transition Analysis Reveals TF Activity Related to
Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast . . . . . . . . 271
T.A. Knijnenburg, L.F.A. Wessels, M.J.T. Reinders
An In Silico Analogue of In Vitro Systems Used to Study Epithelial
Cell Morphogenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
M.R. Grant, C.A. Hunt
A Numerical Aggregation Algorithm for the Enzyme-Catalyzed
Substrate Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298
H. Busch, W. Sandmann, V. Wolf
Possibilistic Approach to Biclustering: An Application to
Oligonucleotide Microarray Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
M. Filippone, F. Masulli, S. Rovetta, S. Mitra, H. Banka
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323


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